TSR1

protein-coding

TSR1 ribosome maturation factor, the group of Ribosomal biogenesis factors|Small nucleolar RNA protein coding host genes

Gene summary

Enables RNA binding activity. Predicted to be involved in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in cytosol and nucleoplasm. Predicted to be part of 90S preribosome. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018128.5

Inheritance

ClinVar variants

U:151B:9

Top phenotype

TSR1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr17:2,322,396-2,336,657

External References & Databases

Ensembl (ENSG00000167721)

Transcript & Mutation Effects

hg38 • Region Span ~14.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

idiopathic spontaneous coronary artery dissectionLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0007385

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSR1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 140

not providedTotal: 9

TSR1-related disorderTotal: 3

Primary microcephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018128.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar		1 clinvar	5
missense			141 clinvar	6 clinvar	2 clinvar	149
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	151	6	3	160

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018128.5	RefSeq	NP_060598.3	15	MANE Select
ENST00000301364.10	Ensembl	ENSP00000301364.4	15	MANE Select
ENST00000571806.1	Ensembl	ENSP00000461498.1	2	Standard
ENST00000575049.1	Ensembl	ENSP00000461192.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Molecular Function

RNA binding
GTPase activity
GTP binding
U3 snoRNA binding

Cellular Component

nucleoplasm
nucleolus
cytosol
preribosome, small subunit precursor

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301364
Coding exons: 15
Length: 15005
Individuals with no LoFs: 125585
Homozygous LoFs: 0
Heterozygous LoFs: 163
Defined: 125748
p: 0.000648

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0643	445	441	1.01	0.0000224	5299
Missense (PolyPhen)		144	149.63	0.96235		1754
Synonymous	-0.334	166	161	1.03	0.00000803	1519
Loss of Function	0.924	35	41.4	0.845	0.00000229	470

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00096	0.00095	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0012	0.0010	notable
Finnish	0.00075	0.00074	rare
European (Non-Finnish)	0.00046	0.00046	rare
South Asian	0.00074	0.00072	rare
Other	0.0016	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required during maturation of the 40S ribosomal subunit in the nucleolus. {ECO:0000250}.;

Recessive Scores

pRec: 0.131

Intolerance Scores

LoFtool: 0.985
RVIS EVS: 0.01
RVIS percentile EVS: 54.1

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.724

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium